The environmental DNA (eDNA) dataset includes records from water samples collected across Pristine Seas expeditions to detect and characterize marine biodiversity using molecular techniques. eDNA captures genetic material shed by organisms into the environment (e.g., via skin, scales, gametes, or excretions), enabling the detection of species that are otherwise difficult to observe using traditional survey methods.
Tables
Sites (edna.sites)
The edna.sites table contains one row per environmental DNA (eDNA) sampling site. Each site represents a distinct point in space and time and serves as the primary spatial unit for eDNA fieldwork. Within a site, multiple water samples (replicates) may be collected across different depth strata, recorded in the corresponding edna.stations table.
This table captures spatial metadata, sampling platform, habitat descriptors, and effort summaries. It supports integration with other methods (e.g., UVS, BRUVs) through common spatial fields and an optional pairing field (paired_ps_site_id).
Table 1: Additional fields in the edna.sites table (eDNA-specific site metadata)
Field
Type
Required
Description
habitat
STRING
true
Dominant habitat type. Allowed values: fore reef, back reef, fringing reef, patch reef, reef flat, channel, seagrass, rocky reef, open water, bay, estuary, mangrove, other.
exposure
STRING
true
Wind and wave exposure. Allowed values: windward, leeward, lagoon, other.
paired_ps_site_id
STRING
false
Foreign key to a related site (e.g., from uvs or pbruvs), if applicable.
n_stations
INTEGER
true
Number of depth-stratified eDNA stations at this site.
n_samples
INTEGER
true
Total number of water samples (replicates) collected at the site.
site_photos
STRING
false
Path to site photo folder, if available (e.g., eDNA/site_photos/COL-2022-edna-001).
Stations (edna.stations)
Samples (edna.stations)
Source Code
---title: "eDNA Dataset"format: html: theme: lux self-contained: true code-fold: true toc: true toc-depth: 3 toc-location: right number-sections: true number-depth: 3---```{r setup, message = F, warning = F, fig.width = 10, fig.height = 10, echo = F}options(scipen = 999)library(PristineSeasR)library(bigrquery)library(gt)library(gtExtras)library(tibble)library(tidyverse)library(dplyr)library(ggplot2)library(plotly)library(lubridate)knitr::opts_chunk$set(eval = F, warning = F, message = F, include = F, echo = F)ps_paths <- PristineSeasR::get_sci_drive_paths()prj_path <- file.path(ps_paths$projects, "legacy-db")ps_data_path <- ps_paths$datasetsbigrquery::bq_auth(email = "marine.data.science@ngs.org")project_id <- "pristine-seas"bq_connection <- DBI::dbConnect(bigrquery::bigquery(), project = project_id)```#### OverviewThe environmental DNA (eDNA) dataset includes records from water samples collected across Pristine Seas expeditions to detect and characterize marine biodiversity using molecular techniques. eDNA captures genetic material shed by organisms into the environment (e.g., via skin, scales, gametes, or excretions), enabling the detection of species that are otherwise difficult to observe using traditional survey methods.------------------------------------------------------------------------#### Tables ------------------------------------------------------------------------##### Sites (`edna.sites`)The `edna.sites` table contains one row per environmental DNA (eDNA) sampling site. Each site represents a distinct point in space and time and serves as the primary spatial unit for eDNA fieldwork. Within a site, multiple water samples (replicates) may be collected across different depth strata, recorded in the corresponding `edna.stations` table.This table captures spatial metadata, sampling platform, habitat descriptors, and effort summaries. It supports integration with other methods (e.g., UVS, BRUVs) through common spatial fields and an optional pairing field (paired_ps_site_id).```{r edna_fields, eval = T, include = T}#| label: tbl-edna.sites-schema#| tbl-cap: "Additional fields in the `edna.sites` table (eDNA-specific site metadata)"edna_sites_fields <- tribble( ~field, ~type, ~required, ~description, "habitat", "STRING", TRUE, "Dominant habitat type. Allowed values: *fore reef*, *back reef*, *fringing reef*, *patch reef*, *reef flat*, *channel*, *seagrass*, *rocky reef*, *open water*, *bay*, *estuary*, *mangrove*, *other*.", "exposure", "STRING", TRUE, "Wind and wave exposure. Allowed values: *windward*, *leeward*, *lagoon*, *other*.", "paired_ps_site_id", "STRING", FALSE, "Foreign key to a related site (e.g., from `uvs` or `pbruvs`), if applicable.", "n_stations", "INTEGER", TRUE, "Number of depth-stratified eDNA stations at this site.", "n_samples", "INTEGER", TRUE, "Total number of water samples (replicates) collected at the site.", "site_photos", "STRING", FALSE, "Path to site photo folder, if available (e.g., `eDNA/site_photos/COL-2022-edna-001`).")gt(edna_sites_fields) |> cols_label(field = md("**Field**"), type = md("**Type**"), required = md("**Required**"), description = md("**Description**")) |> cols_width(field ~ px(200), type ~ px(100), required ~ px(80), description ~ px(500)) |> data_color(columns = c(field), fn = scales::col_factor(palette = c("#f6f6f6"), domain = NULL) ) |> tab_options(table.font.size = px(13), table.width = pct(100)) |> fmt_tf(columns = required, tf_style = "true-false") |> fmt_markdown(columns = description) |> gt_theme_nytimes()```##### Stations (`edna.stations`)##### Samples (`edna.stations`)